Sample summary
Input data: breastmilk samples (BM1, BM2, BM3)
- n samples = 1124
- n taxa: genera = 350; variants = 1712
- n taxa (rarefied): genera = 349; variants = 1711
Statistical methods for mixed-effects models
- Linear mixed-effects models fit with family ID as a random effect
- Association with ORV outcome determined by comparing fit of model with country/age vs model with age alone
Alpha diversity
Column
Seroconversion
Longitudinal plots - Shannon
Longitudinal plots - richness
Blue = seroconversion+, Orange = seroconversion-.
N by country
, , = IND
BM1 BM2 BM3
0 193 175 168
1 79 70 62
, , = MLW
BM1 BM2 BM3
0 61 54 56
1 19 16 11
, , = UK
BM1 BM2 BM3
0 21 16 18
1 21 18 15
, , = IND (neo+)
BM1 BM2 BM3
0 102 90 91
1 47 42 35
, , = IND (neo-)
BM1 BM2 BM3
0 90 84 76
1 32 28 27P values, cross-sectional analayses - Shannon
variable n total (r) responders non-responders RR (95% CI) p
1 Shannon 272 (79) 1.8 (0.6) 1.8 (0.6) 0.95 (0.67-1.29) 0.77009
2 Shannon 245 (70) 2.1 (0.6) 2.0 (0.5) 1.14 (0.79-1.57) 0.46842
3 Shannon 230 (62) 2.0 (0.5) 2.0 (0.5) 0.85 (0.53-1.27) 0.44584
4 Shannon 80 (19) 1.9 (0.6) 1.7 (0.7) 1.37 (0.78-2.16) 0.25498
5 Shannon 70 (16) 1.5 (0.5) 1.9 (0.5) 0.23 (0.06-0.69) 0.01119
6 Shannon 67 (11) 1.9 (0.5) 1.8 (0.5) 1.36 (0.47-3.00) 0.53177
7 Shannon 42 (21) 1.2 (0.4) 1.2 (0.5) 1.08 (0.48-1.63) 0.80502
8 Shannon 34 (18) 1.4 (0.5) 1.4 (0.6) 0.97 (0.41-1.50) 0.91999
9 Shannon 33 (15) 1.4 (0.5) 1.5 (0.6) 0.78 (0.29-1.41) 0.49574
10 Shannon 149 (47) 1.8 (0.6) 1.8 (0.6) 1.01 (0.65-1.46) 0.95330
11 Shannon 132 (42) 2.1 (0.6) 2.0 (0.5) 1.40 (0.93-1.93) 0.10919
12 Shannon 126 (35) 1.9 (0.5) 2.0 (0.5) 0.88 (0.46-1.48) 0.64841
13 Shannon 122 (32) 1.8 (0.6) 1.8 (0.6) 0.87 (0.49-1.42) 0.60958
14 Shannon 112 (28) 2.0 (0.5) 2.1 (0.5) 0.78 (0.37-1.44) 0.45902
15 Shannon 103 (27) 2.1 (0.5) 2.1 (0.5) 0.84 (0.40-1.52) 0.59319
country sample
1 India BM1
2 India BM2
3 India BM3
4 Malawi BM1
5 Malawi BM2
6 Malawi BM3
7 UK BM1
8 UK BM2
9 UK BM3
10 India (neo+) BM1
11 India (neo+) BM2
12 India (neo+) BM3
13 India (neo-) BM1
14 India (neo-) BM2
15 India (neo-) BM3P values, cross-sectional analayses - richness
variable n total (r) responders non-responders RR (95% CI) p
1 Observed 272 (79) 27.1 (11.8) 26.5 (11.5) 1.07 (0.69-1.55) 0.73646
2 Observed 245 (70) 28.4 (9.4) 26.6 (10.9) 1.45 (0.92-2.08) 0.10866
3 Observed 230 (62) 25.9 (8.4) 25.4 (9.4) 1.19 (0.68-1.88) 0.52412
4 Observed 80 (19) 25.7 (11.6) 23.4 (12.7) 1.35 (0.67-2.39) 0.39364
5 Observed 70 (16) 21.3 (9.9) 25.4 (11.1) 0.43 (0.11-1.26) 0.14496
6 Observed 67 (11) 28.6 (10.9) 26.1 (10.6) 1.66 (0.42-4.15) 0.44668
7 Observed 42 (21) 12.2 (4.6) 12.7 (7.2) 1.01 (0.43-1.58) 0.98400
8 Observed 34 (18) 14.7 (6.9) 18.4 (8.2) 0.45 (0.08-1.09) 0.13654
9 Observed 33 (15) 14.6 (4.8) 16.6 (7.1) 0.77 (0.19-1.64) 0.61304
10 Observed 149 (47) 27.9 (12.1) 25.5 (11.3) 1.36 (0.82-1.98) 0.22406
11 Observed 132 (42) 29.4 (9.7) 26.2 (11.1) 1.71 (1.02-2.40) 0.05182
12 Observed 126 (35) 25.9 (7.8) 24.6 (9.6) 1.48 (0.71-2.44) 0.27074
13 Observed 122 (32) 26.1 (11.5) 27.5 (11.7) 0.75 (0.34-1.44) 0.42038
14 Observed 112 (28) 27.0 (9.0) 27.1 (10.8) 1.06 (0.45-2.07) 0.87477
15 Observed 103 (27) 25.8 (9.3) 26.1 (9.1) 0.95 (0.40-1.92) 0.90272
country sample
1 India BM1
2 India BM2
3 India BM3
4 Malawi BM1
5 Malawi BM2
6 Malawi BM3
7 UK BM1
8 UK BM2
9 UK BM3
10 India (neo+) BM1
11 India (neo+) BM2
12 India (neo+) BM3
13 India (neo-) BM1
14 India (neo-) BM2
15 India (neo-) BM3P values, longitudinal mixed-effects models
Shannon log(Observed)
IND 0.8925 0.1791
IND (neo+) 0.4638 0.0192
IND (neo-) 0.3305 0.6376
MLW 0.8113 0.8196
UK 0.7774 0.3284Post-ORV RV-IgA
Week of life 1
Correlation coefficients values
India India_exposed India_unexposed Malawi UK
Shannon -0.0757 -0.0575 -0.1209 0.0783 0.1141
log(richness) -0.0925 -0.0533 -0.1123 0.0677 -0.0341P values
India India_exposed India_unexposed Malawi UK
Shannon 0.2133 0.4859 0.1847 0.4899 0.4553
log(richness) 0.1282 0.5185 0.2180 0.5505 0.8240N
India India_neo_pos India_neo_neg Malawi UK
1 272 149 122 80 45
2 272 149 122 80 45Week of life 7
Correlation coefficients values
India India_exposed India_unexposed Malawi UK
Shannon -0.0753 -0.0526 -0.0748 -0.1939 0.1138
log(richness) 0.0131 0.0151 0.0237 -0.1916 -0.2508P values
India India_exposed India_unexposed Malawi UK
Shannon 0.2400 0.5490 0.4333 0.1078 0.5025
log(richness) 0.8383 0.8639 0.8039 0.1121 0.1343N
India India_neo_pos India_neo_neg Malawi UK
1 245 132 112 70 37
2 245 132 112 70 37Week of life 11
Correlation coefficients values
India India_exposed India_unexposed Malawi UK
Shannon -0.1097 -0.0566 -0.0118 0.0720 -0.1496
log(richness) 0.0248 0.0776 0.0603 0.0927 -0.1911P values
India India_exposed India_unexposed Malawi UK
Shannon 0.0969 0.5289 0.9062 0.5625 0.3840
log(richness) 0.7086 0.3875 0.5453 0.4554 0.2642N
India India_neo_pos India_neo_neg Malawi UK
1 230 126 103 67 36
2 230 126 103 67 36Dose 1 shedding
Longitudinal plots - Shannon
Longitudinal plots - richness
N by country
, , = IND
BM1 BM2
0 195 177
1 77 68
, , = MLW
BM1 BM2
0 35 32
1 42 35
, , = UK
BM1 BM2
0 0 0
1 0 0
, , = IND (neo+)
BM1 BM2
0 119 106
1 28 24
, , = IND (neo-)
BM1 BM2
0 74 69
1 48 43P values, cross-sectional analayses - Shannon
variable n total (r) responders non-responders RR (95% CI) p
1 Shannon 272 (77) 1.9 (0.6) 1.8 (0.6) 1.28 (0.93-1.67) 0.12292
2 Shannon 245 (68) 2.1 (0.5) 2.0 (0.5) 1.26 (0.88-1.72) 0.19800
3 Shannon 0 (0) <NA> <NA> <NA> <NA>
4 Shannon 77 (42) 1.7 (0.6) 1.9 (0.7) 0.83 (0.54-1.13) 0.27120
5 Shannon 67 (35) 1.8 (0.5) 1.8 (0.6) 0.99 (0.60-1.37) 0.95574
6 Shannon 0 (0) <NA> <NA> <NA> <NA>
7 Shannon 0 (0) <NA> <NA> <NA> <NA>
8 Shannon 0 (0) <NA> <NA> <NA> <NA>
9 Shannon 0 (0) <NA> <NA> <NA> <NA>
10 Shannon 147 (28) 1.9 (0.6) 1.8 (0.6) 1.19 (0.66-1.96) 0.54339
11 Shannon 130 (24) 2.1 (0.6) 2.0 (0.6) 1.30 (0.69-2.25) 0.40581
12 Shannon 0 (0) <NA> <NA> <NA> <NA>
13 Shannon 122 (48) 1.9 (0.6) 1.8 (0.6) 1.30 (0.91-1.70) 0.14532
14 Shannon 112 (43) 2.1 (0.5) 2.0 (0.5) 1.24 (0.78-1.73) 0.32884
15 Shannon 0 (0) <NA> <NA> <NA> <NA>
country sample
1 India BM1
2 India BM2
3 India BM3
4 Malawi BM1
5 Malawi BM2
6 Malawi BM3
7 UK BM1
8 UK BM2
9 UK BM3
10 India (neo+) BM1
11 India (neo+) BM2
12 India (neo+) BM3
13 India (neo-) BM1
14 India (neo-) BM2
15 India (neo-) BM3P values, cross-sectional analayses - richness
variable n total (r) responders non-responders RR (95% CI) p
1 Observed 272 (77) 29.5 (12.4) 25.4 (11.0) 1.61 (1.11-2.16) 0.01735
2 Observed 245 (68) 27.2 (9.5) 27.1 (10.9) 1.10 (0.66-1.69) 0.69248
3 Observed 0 (0) <NA> <NA> <NA> <NA>
4 Observed 77 (42) 22.5 (11.6) 25.6 (12.2) 0.74 (0.39-1.11) 0.17996
5 Observed 67 (35) 25.5 (13.0) 23.9 (10.7) 1.08 (0.60-1.51) 0.74364
6 Observed 0 (0) <NA> <NA> <NA> <NA>
7 Observed 0 (0) <NA> <NA> <NA> <NA>
8 Observed 0 (0) <NA> <NA> <NA> <NA>
9 Observed 0 (0) <NA> <NA> <NA> <NA>
10 Observed 147 (28) 28.4 (13.3) 25.6 (11.1) 1.39 (0.66-2.54) 0.37163
11 Observed 130 (24) 27.2 (9.9) 27.2 (10.9) 1.12 (0.46-2.38) 0.78807
12 Observed 0 (0) <NA> <NA> <NA> <NA>
13 Observed 122 (48) 30.4 (12.0) 25.1 (10.9) 1.63 (1.10-2.08) 0.02291
14 Observed 112 (43) 27.3 (9.4) 27.0 (11.0) 1.11 (0.59-1.72) 0.71270
15 Observed 0 (0) <NA> <NA> <NA> <NA>
country sample
1 India BM1
2 India BM2
3 India BM3
4 Malawi BM1
5 Malawi BM2
6 Malawi BM3
7 UK BM1
8 UK BM2
9 UK BM3
10 India (neo+) BM1
11 India (neo+) BM2
12 India (neo+) BM3
13 India (neo-) BM1
14 India (neo-) BM2
15 India (neo-) BM3P values, longitudinal mixed-effects models
Shannon log(Observed)
IND 0.0623 0.0503
IND (neo+) 0.3340 0.3866
IND (neo-) 0.1005 0.0583
MLW 0.3646 0.3763Beta diversity
Column
Unweighted
Seroconversion
R2 p n country week full outcome
IND_BM1 0.3788083 0.384 272 IND 1 1 seroconversion
IND_BM2 0.4746925 0.269 245 IND 7 1 seroconversion
IND_BM3 0.3475465 0.752 230 IND 11 1 seroconversion
MLW_BM1 1.2432429 0.455 80 MLW 1 1 seroconversion
MLW_BM2 1.8015592 0.174 70 MLW 7 1 seroconversion
MLW_BM3 0.9029032 0.932 67 MLW 11 1 seroconversion
UK_BM1 1.7106198 0.794 42 UK 1 1 seroconversion
UK_BM2 4.3098177 0.114 34 UK 7 1 seroconversion
UK_BM3 1.7661924 0.887 33 UK 11 1 seroconversion
INDexp_BM1 0.7405885 0.283 149 IND (neo+) 1 0 seroconversion
INDexp_BM2 0.8373905 0.306 132 IND (neo+) 7 0 seroconversion
INDexp_BM3 0.5392045 0.881 126 IND (neo+) 11 0 seroconversion
INDunexp_BM1 0.6115097 0.825 122 IND (neo-) 1 0 seroconversion
INDunexp_BM2 0.6878895 0.816 112 IND (neo-) 7 0 seroconversion
INDunexp_BM3 1.3375167 0.101 103 IND (neo-) 11 0 seroconversion
RV-IgA
R2 p n country week full outcome
IND_BM1 0.5008963 0.096 272 IND 1 1 RV-IgA (post-ORV)
IND_BM2 0.5394922 0.149 245 IND 7 1 RV-IgA (post-ORV)
IND_BM3 0.4191227 0.530 230 IND 11 1 RV-IgA (post-ORV)
MLW_BM1 0.9926848 0.734 80 MLW 1 1 RV-IgA (post-ORV)
MLW_BM2 2.0630760 0.093 70 MLW 7 1 RV-IgA (post-ORV)
MLW_BM3 0.7910595 0.965 67 MLW 11 1 RV-IgA (post-ORV)
UK_BM1 2.2612923 0.465 45 UK 1 1 RV-IgA (post-ORV)
UK_BM2 5.9977991 0.005 37 UK 7 1 RV-IgA (post-ORV)
UK_BM3 2.7042128 0.486 36 UK 11 1 RV-IgA (post-ORV)
INDexp_BM1 0.7849895 0.265 149 IND (neo+) 1 0 RV-IgA (post-ORV)
INDexp_BM2 0.6647328 0.646 132 IND (neo+) 7 0 RV-IgA (post-ORV)
INDexp_BM3 0.6365908 0.752 126 IND (neo+) 11 0 RV-IgA (post-ORV)
INDunexp_BM1 0.6382606 0.789 122 IND (neo-) 1 0 RV-IgA (post-ORV)
INDunexp_BM2 0.9788583 0.349 112 IND (neo-) 7 0 RV-IgA (post-ORV)
INDunexp_BM3 1.2387376 0.150 103 IND (neo-) 11 0 RV-IgA (post-ORV)
Dose 1 shedding
R2 p n country week full outcome
IND_BM1 0.4633303 0.166 272 IND 1 1 dose 1 shedding
IND_BM2 0.3745513 0.592 245 IND 7 1 dose 1 shedding
MLW_BM1 1.6554250 0.190 77 MLW 1 1 dose 1 shedding
MLW_BM2 1.0958493 0.793 67 MLW 7 1 dose 1 shedding
INDexp_BM1 0.3271173 0.991 147 IND (neo+) 1 0 dose 1 shedding
INDexp_BM2 0.6294284 0.728 130 IND (neo+) 7 0 dose 1 shedding
INDunexp_BM1 1.2889788 0.036 122 IND (neo-) 1 0 dose 1 shedding
INDunexp_BM2 0.7920155 0.649 112 IND (neo-) 7 0 dose 1 shedding
Weighted
Seroconversion
R2 p n country week full outcome
IND_BM1 0.4073267 0.330 272 IND 1 1 seroconversion
IND_BM2 0.3559273 0.521 245 IND 7 1 seroconversion
IND_BM3 0.5876315 0.160 230 IND 11 1 seroconversion
MLW_BM1 0.8355983 0.816 80 MLW 1 1 seroconversion
MLW_BM2 3.0451683 0.022 70 MLW 7 1 seroconversion
MLW_BM3 0.5401890 0.975 67 MLW 11 1 seroconversion
UK_BM1 2.6524856 0.312 42 UK 1 1 seroconversion
UK_BM2 3.6408664 0.282 34 UK 7 1 seroconversion
UK_BM3 1.5260302 0.883 33 UK 11 1 seroconversion
INDexp_BM1 0.3559372 0.850 149 IND (neo+) 1 0 seroconversion
INDexp_BM2 0.5027904 0.743 132 IND (neo+) 7 0 seroconversion
INDexp_BM3 1.0114751 0.230 126 IND (neo+) 11 0 seroconversion
INDunexp_BM1 2.6860734 0.007 122 IND (neo-) 1 0 seroconversion
INDunexp_BM2 0.8562030 0.449 112 IND (neo-) 7 0 seroconversion
INDunexp_BM3 0.6743814 0.740 103 IND (neo-) 11 0 seroconversionRV-IgA
R2 p n country week full outcome
IND_BM1 0.5684348 0.150 272 IND 1 1 RV-IgA (post-ORV)
IND_BM2 0.4020393 0.412 245 IND 7 1 RV-IgA (post-ORV)
IND_BM3 0.8380610 0.046 230 IND 11 1 RV-IgA (post-ORV)
MLW_BM1 0.7861263 0.846 80 MLW 1 1 RV-IgA (post-ORV)
MLW_BM2 1.9625820 0.160 70 MLW 7 1 RV-IgA (post-ORV)
MLW_BM3 0.6061001 0.960 67 MLW 11 1 RV-IgA (post-ORV)
UK_BM1 3.2182804 0.197 45 UK 1 1 RV-IgA (post-ORV)
UK_BM2 5.5700825 0.064 37 UK 7 1 RV-IgA (post-ORV)
UK_BM3 1.4027478 0.839 36 UK 11 1 RV-IgA (post-ORV)
INDexp_BM1 0.3493443 0.852 149 IND (neo+) 1 0 RV-IgA (post-ORV)
INDexp_BM2 0.4653291 0.809 132 IND (neo+) 7 0 RV-IgA (post-ORV)
INDexp_BM3 1.0262361 0.239 126 IND (neo+) 11 0 RV-IgA (post-ORV)
INDunexp_BM1 3.3948972 0.002 122 IND (neo-) 1 0 RV-IgA (post-ORV)
INDunexp_BM2 0.6083572 0.762 112 IND (neo-) 7 0 RV-IgA (post-ORV)
INDunexp_BM3 0.6870211 0.734 103 IND (neo-) 11 0 RV-IgA (post-ORV)Dose 1 shedding
R2 p n country week full outcome
IND_BM1 0.2283407 0.757 272 IND 1 1 dose 1 shedding
IND_BM2 0.5387310 0.186 245 IND 7 1 dose 1 shedding
MLW_BM1 1.3435442 0.383 77 MLW 1 1 dose 1 shedding
MLW_BM2 1.4937325 0.442 67 MLW 7 1 dose 1 shedding
INDexp_BM1 0.3806246 0.811 147 IND (neo+) 1 0 dose 1 shedding
INDexp_BM2 0.8939386 0.277 130 IND (neo+) 7 0 dose 1 shedding
INDunexp_BM1 0.7639850 0.456 122 IND (neo-) 1 0 dose 1 shedding
INDunexp_BM2 0.7878907 0.513 112 IND (neo-) 7 0 dose 1 sheddingDifferential taxa
Column
Seroconversion
Genus- and RSV-level models
Summary plot
Differential genera - Fisher’s test or Aldex2 (FDR p <0.05)
Differential RSVs - Fisher’s test or Aldex2 (FDR p <0.05)
RV-IgA
Genus- and RSV-level models
Summary plot
Differential genera - Fisher’s test or Aldex2 (FDR p <0.05)
Differential RSVs - Fisher’s test or Aldex2 (FDR p <0.05)
Dose 1 shedding
Genus- and RSV-level models
Summary plot
Differential genera - Fisher’s test or Aldex2 (FDR p <0.05)
Differential RSVs - Fisher’s test or Aldex2 (FDR p <0.05)
Summary figures
Seroconversion
RV-IgA
Dose 1 shedding
Longitudinal abundance comparisons
Immunogenicity
Number of infants/taxa included in longitudinal models:
- India (full), n infants: 300; n samples: 747; n taxa: 53
- India (exposed), n infants: 164; n samples: 407; n taxa: 56
- India (unexposed), n infants: 135; n samples: 337; n taxa: 49
- Malawi, n infants: 97; n samples: 217; n taxa: 50
- UK, n infants: 43; n samples: 109; n taxa: 31
India
negatively correlated ns positively correlated
age 6 5 42
IgA 0 53 0
seroconv 0 53 0 taxon Estimate Std.Error
1 Bifidobacterium 0.032 0.010
2 Streptococcus 0.027 0.006
3 Staphylococcus -0.131 0.008
4 Veillonella 0.179 0.009
5 Lactobacillus 0.111 0.010
6 Collinsella 0.045 0.008
7 Haemophilus -0.035 0.008
8 Klebsiella -0.092 0.009
10 Rothia 0.019 0.009
11 Gemella -0.052 0.008
12 Bacillus 0.061 0.009
13 Pseudomonas 0.036 0.009
14 Cutibacterium 0.078 0.009
15 Enterobacter -0.043 0.007
16 Acinetobacter 0.026 0.011
17 Enhydrobacter 0.075 0.008
19 Hydrogenophilus 0.128 0.009
20 Bradyrhizobium 0.070 0.009
21 Dermacoccus 0.023 0.008
22 Paracoccus 0.052 0.009
23 Granulicatella 0.104 0.008
24 Micrococcus 0.070 0.008
25 Kocuria 0.080 0.008
26 S31 0.141 0.009
27 Janibacter 0.052 0.008
28 Aeromonas 0.068 0.009
29 Aerococcus 0.039 0.007
30 Shewanella 0.086 0.008
31 Chryseobacterium 0.055 0.008
32 Cloacibacterium 0.113 0.008
34 Exiguobacterium 0.080 0.008
36 Alishewanella 0.021 0.009
37 Brachybacterium 0.043 0.008
38 Rubellimicrobium 0.068 0.009
39 Brevundimonas 0.086 0.009
40 Stenotrophomonas 0.057 0.008
41 Geobacillus 0.103 0.009
42 Bergeyella 0.025 0.007
43 Moraxella 0.039 0.008
44 Saccharopolyspora 0.058 0.009
45 Anaerococcus 0.020 0.009
47 Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium 0.046 0.008
48 Qipengyuania 0.095 0.010
49 Brevibacterium 0.052 0.008
50 Ornithinimicrobium 0.090 0.009
51 Deinococcus 0.112 0.001
52 unassigned -0.070 0.009
53 Sphingomonas 0.132 0.009
padj comparison
1 9.367442e-04 age
2 1.209487e-05 age
3 5.123333e-45 age
4 8.480000e-61 age
5 5.300000e-23 age
6 2.005405e-07 age
7 2.252500e-05 age
8 5.653333e-20 age
10 3.157447e-02 age
11 1.519333e-09 age
12 7.746154e-12 age
13 2.068293e-04 age
14 2.090556e-17 age
15 1.026875e-08 age
16 2.765217e-02 age
17 2.789474e-17 age
19 6.738571e-36 age
20 4.795238e-15 age
21 3.734091e-03 age
22 3.273529e-08 age
23 1.855000e-29 age
24 2.040500e-16 age
25 4.858333e-22 age
26 5.167500e-42 age
27 5.110714e-11 age
28 2.312727e-14 age
29 4.391429e-08 age
30 2.544000e-24 age
31 3.729630e-11 age
32 1.855000e-36 age
34 1.514286e-21 age
36 1.531111e-02 age
37 5.741667e-08 age
38 3.312500e-12 age
39 1.309412e-19 age
40 7.746154e-12 age
41 9.422222e-26 age
42 6.309524e-04 age
43 6.973684e-06 age
44 8.955172e-11 age
45 3.312500e-02 age
47 1.043939e-08 age
48 9.606250e-20 age
49 1.538710e-09 age
50 1.514286e-21 age
51 3.869000e-276 age
52 3.686957e-14 age
53 7.314000e-41 ageSummary statistics
[1] "No significant differences according to ORV outcome"India (exposed)
negatively correlated ns positively correlated
age 8 11 37
IgA 0 56 0
seroconv 0 56 0 taxon Estimate Std.Error
2 Streptococcus 0.038 0.008
3 Staphylococcus -0.128 0.011
4 Veillonella 0.193 0.012
5 Lactobacillus 0.097 0.015
7 Haemophilus -0.037 0.013
8 Klebsiella -0.067 0.013
10 Rothia 0.032 0.011
11 Gemella -0.082 0.009
12 Bacillus 0.066 0.012
13 Pseudomonas 0.028 0.012
14 Cutibacterium 0.059 0.012
15 Enterobacter -0.035 0.010
17 Enhydrobacter 0.095 0.011
18 Corynebacterium_1 0.027 0.011
19 Hydrogenophilus 0.149 0.012
20 Bradyrhizobium 0.088 0.012
21 Blautia -0.025 0.012
22 Dermacoccus 0.059 0.012
23 Paracoccus 0.056 0.013
24 Granulicatella 0.159 0.009
25 Micrococcus 0.080 0.011
26 Kocuria 0.068 0.010
27 S31 0.125 0.014
29 Aeromonas 0.032 0.011
30 Aerococcus 0.067 0.010
31 Shewanella 0.041 0.010
32 Chryseobacterium 0.039 0.012
33 Cloacibacterium 0.101 0.012
34 Rheinheimera 0.050 0.011
35 Exiguobacterium 0.085 0.011
38 Brachybacterium 0.035 0.011
39 Rubellimicrobium 0.114 0.014
40 Brevundimonas 0.103 0.012
41 Stenotrophomonas 0.076 0.018
42 Geobacillus 0.059 0.018
43 Bergeyella 0.045 0.010
45 Neisseria -0.027 0.012
46 Saccharopolyspora 0.144 0.011
47 Anaerococcus -0.025 0.012
49 Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium 0.038 0.011
50 Qipengyuania 0.095 0.014
52 Ornithinimicrobium 0.094 0.012
53 Deinococcus 0.063 0.002
54 Novosphingobium 0.058 0.010
56 Sphingomonas 0.127 0.014
padj comparison
2 6.844444e-06 age
3 7.653333e-25 age
4 4.106667e-37 age
5 5.333333e-10 age
7 5.887179e-03 age
8 2.464000e-06 age
10 6.160000e-03 age
11 3.304000e-15 age
12 2.678261e-07 age
13 3.255814e-02 age
14 1.330000e-06 age
15 1.218824e-03 age
17 1.773333e-14 age
18 2.048780e-02 age
19 4.144000e-25 age
20 3.325000e-11 age
21 4.106667e-02 age
22 6.030769e-06 age
23 4.666667e-05 age
24 5.320000e-42 age
25 7.155556e-11 age
26 8.252632e-11 age
27 1.400000e-16 age
29 5.010526e-03 age
30 4.941176e-11 age
31 1.417500e-04 age
32 2.333333e-03 age
33 3.304000e-15 age
34 1.980000e-05 age
35 1.082667e-11 age
38 3.935135e-03 age
39 1.680000e-14 age
40 2.153846e-14 age
41 5.419355e-05 age
42 1.392000e-03 age
43 4.055172e-05 age
45 3.255814e-02 age
46 9.520000e-31 age
47 4.106667e-02 age
49 8.993939e-04 age
50 4.760000e-10 age
52 3.160000e-13 age
53 8.960000e-74 age
54 2.240000e-08 age
56 1.400000e-16 ageSummary statistics
[1] "No significant differences according to ORV outcome"India (unexposed)
negatively correlated ns positively correlated
age 5 9 35
IgA 0 49 0
seroconv 0 49 0 taxon Estimate Std.Error padj comparison
1 Bifidobacterium 0.058 0.014 1.102500e-04 age
3 Staphylococcus -0.139 0.012 4.704000e-22 age
4 Veillonella 0.166 0.014 7.840000e-25 age
5 Lactobacillus 0.158 0.016 5.390000e-18 age
6 Collinsella 0.078 0.013 1.653750e-08 age
7 Haemophilus 0.046 0.010 6.533333e-06 age
8 Klebsiella -0.163 0.013 3.332000e-25 age
10 Gemella -0.061 0.013 7.669565e-06 age
11 Bacillus 0.053 0.012 2.744000e-05 age
12 Pseudomonas 0.046 0.015 2.994444e-03 age
13 Cutibacterium 0.103 0.013 6.236364e-13 age
14 Acinetobacter 0.055 0.014 1.738710e-04 age
15 Enhydrobacter 0.039 0.013 3.840541e-03 age
17 Hydrogenophilus 0.095 0.013 7.513333e-11 age
19 Paracoccus 0.048 0.013 3.891176e-04 age
20 Granulicatella 0.058 0.013 2.654167e-05 age
21 Micrococcus 0.058 0.012 2.836842e-06 age
22 Kocuria 0.091 0.012 1.820000e-11 age
23 S31 0.111 0.012 2.123333e-15 age
25 Aeromonas 0.119 0.014 3.969000e-15 age
26 Shewanella 0.067 0.015 3.580769e-05 age
27 Chryseobacterium 0.064 0.011 9.511765e-08 age
28 Cloacibacterium 0.127 0.012 8.166667e-21 age
30 Exiguobacterium 0.037 0.013 6.247500e-03 age
31 Alishewanella 0.068 0.013 9.800000e-07 age
32 Brachybacterium 0.056 0.012 6.533333e-06 age
34 Brevundimonas 0.053 0.014 2.143750e-04 age
35 Stenotrophomonas 0.046 0.012 3.266667e-04 age
37 Moraxella 0.049 0.014 5.320000e-04 age
38 Saccharopolyspora -0.036 0.012 3.868421e-03 age
39 Anaerococcus 0.056 0.014 1.738710e-04 age
40 Comamonas 0.056 0.012 7.669565e-06 age
41 Massilia 0.064 0.016 1.016296e-04 age
43 Chryseomicrobium 0.029 0.010 5.402564e-03 age
44 Qipengyuania 0.103 0.010 5.390000e-18 age
45 Brevibacterium 0.097 0.013 9.800000e-12 age
46 Ornithinimicrobium 0.053 0.013 1.605172e-04 age
47 Deinococcus 0.088 0.012 1.820000e-11 age
48 unassigned -0.137 0.012 4.287500e-22 age
49 Sphingomonas 0.140 0.012 2.776667e-23 ageSummary statistics
[1] "No significant differences according to ORV outcome"Malawi
negatively correlated ns positively correlated
age 10 20 20
IgA 0 49 0
seroconv 1 49 0 taxon Estimate Std.Error padj comparison
2 Streptococcus 0.058 0.010 1.500000e-07 age
3 Staphylococcus -0.122 0.018 1.550000e-09 age
4 Bacteroides 0.041 0.017 2.833333e-02 age
5 Veillonella 0.119 0.018 3.181818e-09 age
6 Lactobacillus 0.163 0.019 9.166667e-13 age
8 Haemophilus -0.046 0.013 9.782609e-04 age
9 Klebsiella -0.118 0.018 1.269231e-08 age
10 Rothia 0.185 0.017 6.875000e-18 age
13 Bacillus -0.117 0.010 1.350000e-20 age
17 Enterobacter -0.184 0.017 4.333333e-18 age
19 Enhydrobacter 0.079 0.017 2.394737e-05 age
21 Agathobacter 0.072 0.016 2.750000e-05 age
23 Subdoligranulum -0.072 0.024 5.384615e-03 age
24 Succinivibrio -0.105 0.015 6.062500e-10 age
26 Ruminococcus_2 -0.074 0.016 3.571429e-05 age
27 Dorea 0.089 0.015 1.062500e-07 age
31 Kocuria 0.092 0.018 2.111111e-06 age
33 Janibacter 0.046 0.016 1.107143e-02 age
34 Aeromonas 0.138 0.013 5.100000e-17 age
35 Prevotella_7 0.122 0.017 2.571429e-10 age
37 Actinomyces 0.073 0.025 7.407407e-03 age
38 Brachybacterium 0.045 0.018 2.413793e-02 age
39 Brevundimonas 0.113 0.018 2.178571e-08 age
41 Stenotrophomonas 0.051 0.013 2.954545e-04 age
42 Bergeyella -0.044 0.013 2.291667e-03 age
44 Citricoccus 0.088 0.014 9.166667e-09 age
45 Methylobacterium 0.055 0.017 2.800000e-03 age
46 Brevibacterium 0.097 0.016 1.033333e-07 age
47 Empedobacter -0.230 0.010 6.500000e-43 age
48 Dietzia 0.167 0.024 1.111111e-09 age
82 Alloprevotella -1.505 0.414 2.250000e-02 seroconvSummary statistics
taxon Estimate Std.Error padj comparison mean prev
82 Alloprevotella -1.505 0.414 0.0225 seroconv 0.254 23UK
negatively correlated ns positively correlated
age 10 9 12
IgA 0 30 0
seroconv 0 30 0 taxon Estimate Std.Error
1 Bifidobacterium 0.047 0.021
3 Staphylococcus -0.102 0.016
4 Bacteroides 0.124 0.019
7 Haemophilus -0.058 0.018
8 Klebsiella 0.114 0.020
9 Rothia 0.144 0.018
10 Gemella -0.106 0.018
11 Pseudomonas 0.142 0.023
13 Enterobacter -0.101 0.026
15 Enhydrobacter 0.157 0.024
17 Dermacoccus 0.070 0.015
18 Granulicatella 0.119 0.023
19 Micrococcus 0.039 0.018
20 Kocuria -0.226 0.025
21 Chryseobacterium -0.218 0.029
24 Lawsonella 0.058 0.015
26 Moraxella -0.064 0.018
27 Neisseria -0.098 0.021
28 Lactococcus 0.101 0.018
29 Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium -0.071 0.026
30 unassigned -0.125 0.012
31 Sphingomonas 0.104 0.025
padj comparison
1 4.790909e-02 age
3 1.860000e-07 age
4 6.716667e-08 age
7 2.936842e-03 age
8 6.200000e-07 age
9 4.650000e-10 age
10 7.130000e-07 age
11 1.860000e-07 age
13 4.456250e-04 age
15 4.836000e-08 age
17 2.623077e-05 age
18 5.425000e-06 age
19 4.790909e-02 age
20 1.209000e-11 age
21 2.015000e-09 age
24 4.558824e-04 age
26 9.644444e-04 age
27 3.764286e-05 age
28 2.282727e-06 age
29 1.410500e-02 age
30 2.294000e-14 age
31 1.570667e-04 ageSummary statistics
[1] "No significant differences according to ORV outcome"Dose 1 shedding
Number of infants/taxa included in longitudinal models:
- India (full), n infants: 296; n samples: 517; n taxa: 53
- India (exposed), n infants: 160; n samples: 277; n taxa: 57
- India (unexposed), n infants: 133; n samples: 234; n taxa: 52
- Malawi, n infants: 88; n samples: 144; n taxa: 51
- UK, n infants: 51; n samples: 89; n taxa: 33
India
ns positively correlated
dose1_shedding 51 2Summary statistics
taxon Estimate Std.Error padj comparison mean prev
19 Hydrogenophilus 0.662 0.198 0.024645 dose1_shedding 0.836 52.0
46 Massilia 1.124 0.278 0.003604 dose1_shedding 0.247 21.3India (exposed)
ns
dose1_shedding 57Summary statistics
[1] "No significant differences according to ORV outcome"India (unexposed)
ns positively correlated
dose1_shedding 51 1Summary statistics
taxon Estimate Std.Error padj comparison mean prev
44 Massilia 1.623 0.328 0.0001196 dose1_shedding 0.399 25.2Malawi
ns
dose1_shedding 51Summary statistics
[1] "No significant differences according to ORV outcome".
Session info
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] FSA_0.9.1 ALDEx2_1.26.0
[3] zCompositions_1.4.0 truncnorm_1.0-8
[5] NADA_1.6-1.1 survival_3.2-13
[7] MASS_7.3-55 sjstats_0.18.0
[9] ggExtra_0.9 formattable_0.2.1
[11] NBZIMM_1.0 inlmisc_0.5.2
[13] decontam_1.14.0 ggtree_3.2.1
[15] wesanderson_0.3.6 phangorn_2.8.1
[17] ape_5.6-1 DECIPHER_2.22.0
[19] RSQLite_2.2.9 Biostrings_2.62.0
[21] XVector_0.34.0 cowplot_1.1.1
[23] scales_1.1.1 RVAideMemoire_0.9-81
[25] DescTools_0.99.44 ggsignif_0.6.3
[27] binom_1.1-1 shiny_1.7.1
[29] randomcoloR_1.1.0.1 DESeq2_1.34.0
[31] SummarizedExperiment_1.24.0 Biobase_2.54.0
[33] MatrixGenerics_1.6.0 GenomicRanges_1.46.1
[35] GenomeInfoDb_1.30.0 IRanges_2.28.0
[37] S4Vectors_0.32.3 BiocGenerics_0.40.0
[39] crossval_1.0.4 UpSetR_1.4.0
[41] labdsv_2.0-1 mgcv_1.8-38
[43] nlme_3.1-155 ggpubr_0.4.0
[45] data.table_1.14.2 corrplot_0.92
[47] ZIBR_0.1 vegan_2.5-7
[49] lattice_0.20-45 permute_0.9-7
[51] randomForest_4.6-14 matrixStats_0.61.0
[53] lme4_1.1-27.1 Matrix_1.4-0
[55] reshape2_1.4.4 pheatmap_1.0.12
[57] DT_0.20 plotly_4.10.0
[59] cluster_2.1.2 tidyr_1.1.4
[61] dplyr_1.0.7 magrittr_2.0.1
[63] plyr_1.8.6 kableExtra_1.3.4
[65] gridExtra_2.3 RColorBrewer_1.1-2
[67] knitr_1.37 ggplot2_3.3.5
[69] phyloseq_1.38.0
loaded via a namespace (and not attached):
[1] estimability_1.3 coda_0.19-4 bit64_4.0.5
[4] DelayedArray_0.20.0 KEGGREST_1.34.0 RCurl_1.98-1.5
[7] generics_0.1.1 terra_1.5-12 proxy_0.4-26
[10] bit_4.0.4 webshot_0.5.2 xml2_1.3.3
[13] httpuv_1.6.5 assertthat_0.2.1 xfun_0.29
[16] hms_1.1.1 jquerylib_0.1.4 evaluate_0.14
[19] promises_1.2.0.1 fansi_1.0.2 igraph_1.2.11
[22] DBI_1.1.2 geneplotter_1.72.0 htmlwidgets_1.5.4
[25] purrr_0.3.4 ellipsis_0.3.2 backports_1.4.1
[28] V8_4.0.0 insight_0.15.0 annotate_1.72.0
[31] vctrs_0.3.8 sjlabelled_1.1.8 abind_1.4-5
[34] cachem_1.0.6 withr_2.4.3 rgdal_1.5-28
[37] emmeans_1.7.2 treeio_1.18.1 svglite_2.0.0
[40] lazyeval_0.2.2 crayon_1.4.2 flexdashboard_0.5.2
[43] genefilter_1.76.0 labeling_0.4.2 pkgconfig_2.0.3
[46] rlang_0.4.12 lifecycle_1.0.1 miniUI_0.1.1.1
[49] modelr_0.1.8 datawizard_0.2.2 aplot_0.1.2
[52] raster_3.5-11 carData_3.0-5 Rhdf5lib_1.16.0
[55] boot_1.3-28 png_0.1-7 viridisLite_0.4.0
[58] parameters_0.16.0 rootSolve_1.8.2.3 bitops_1.0-7
[61] rhdf5filters_1.6.0 blob_1.2.2 stringr_1.4.0
[64] rstatix_0.7.0 gridGraphics_0.5-1 memoise_2.0.1
[67] zlibbioc_1.40.0 compiler_4.1.2 ade4_1.7-18
[70] patchwork_1.1.1 tidyselect_1.1.1 forcats_0.5.1
[73] stringi_1.7.6 highr_0.9 yaml_2.2.1
[76] locfit_1.5-9.4 grid_4.1.2 sass_0.4.0
[79] fastmatch_1.1-3 tools_4.1.2 lmom_2.8
[82] rstudioapi_0.13 foreach_1.5.1 gld_2.6.4
[85] farver_2.1.0 Rtsne_0.15 RcppZiggurat_0.1.6
[88] digest_0.6.29 quadprog_1.5-8 Rcpp_1.0.8
[91] car_3.0-12 broom_0.7.11 performance_0.8.0
[94] later_1.3.0 httr_1.4.2 AnnotationDbi_1.56.2
[97] effectsize_0.6.0 colorspace_2.0-2 rvest_1.0.2
[100] XML_3.99-0.8 splines_4.1.2 yulab.utils_0.0.4
[103] tidytree_0.3.7 expm_0.999-6 sp_1.4-6
[106] multtest_2.50.0 Exact_3.1 ggplotify_0.1.0
[109] systemfonts_1.0.2 xtable_1.8-4 jsonlite_1.7.3
[112] nloptr_1.2.2.3 Rfast_2.0.4 ggfun_0.0.5
[115] R6_2.5.1 pillar_1.6.4 htmltools_0.5.2
[118] mime_0.12 glue_1.6.0 fastmap_1.1.0
[121] minqa_1.2.4 BiocParallel_1.28.3 class_7.3-20
[124] codetools_0.2-18 mvtnorm_1.1-3 utf8_1.2.2
[127] bslib_0.3.1 tibble_3.1.6 curl_4.3.2
[130] rmarkdown_2.11 biomformat_1.22.0 munsell_0.5.0
[133] e1071_1.7-9 rhdf5_2.38.0 GenomeInfoDbData_1.2.7
[136] iterators_1.0.13 haven_2.4.3 sjmisc_2.8.9
[139] gtable_0.3.0 bayestestR_0.11.5 .